He was also found not guilty of sexually assaulting a 42-year-old woman at the filming of a TV show, Test Your Pet, in 2004.
After 26 hours and 16 minutes of deliberations, the jury failed to reach a verdict on four further counts of indecent assault, and was discharged.
The Crown has a week to decide whether to retry those four matters. Prosecutor Jonathan Rees QC asked the court for seven days to "reflect" on the way forward.
The charges relate to alleged incidents involving a 14-year-old girl, a 16-year-old girl, a 13-year-old girl and an 18-year-old woman.
Harris is currently serving a five-year, nine-month jail term after being found guilty by a jury in 2014 of 12 counts of indecently assaulting four women and girls, including one just eight years old.
He is due to be released on parole from the minimum-security Stafford Prison in rural England in May or June.
The seven-woman, five-man jury sitting in the Southwark Crown Court in central London returned the latest verdicts about 12.20pm Wednesday London time, at the end of a trial which started on January 9.
Harris, who wore a dark suit, colourful tie and blue shirt, showed little emotion apart from releasing a deep breath on the second not-guilty verdict.
The charges had related to alleged incidents, characterised by the Crown as groping, at locations across London between 1971 and 2004.
His victims had all alleged Harris had touched them inappropriately.